Sergey Nurk, Brian P Walenz, Arang Rhie, Mitchell R Vollger, Glennis A Logsdon, Robert Grothe, Karen H Miga, Evan E Eichler, Adam M Phillippy, Sergey Koren

Genome Res. 2020 Sep;30(9):1291-1305. doi:10.1101/gr.263566.120

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

“HiCanu modifies the input reads by compressing every homopolymer to a single nucleotide.” “Outputs contigs as “pseudo-haplotypes” that preserve local allelic phasing but may switch between haplotypes”